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- PDB-6pve: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex w... -

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Basic information

Entry
Database: PDB / ID: 6pve
TitleStructure of Nicotinamide N-Methyltransferase (NNMT) in complex with inhibitor LL319
ComponentsNNMT protein
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / Methyltransferase / Inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OZP / Nicotinamide N-methyltransferase / NNMT protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNoinaj, N. / Huang, R. / Chen, D. / Yadav, R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI127793 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117275 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U01CA214649-01 United States
CitationJournal: J.Med.Chem. / Year: 2019
Title: Novel Propargyl-Linked Bisubstrate Analogues as Tight-Binding Inhibitors for NicotinamideN-Methyltransferase.
Authors: Chen, D. / Li, L. / Diaz, K. / Iyamu, I.D. / Yadav, R. / Noinaj, N. / Huang, R.
History
DepositionJul 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NNMT protein
B: NNMT protein
C: NNMT protein
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9788
Polymers125,8644
Non-polymers2,1144
Water8,971498
1
A: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9952
Polymers31,4661
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9952
Polymers31,4661
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9952
Polymers31,4661
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NNMT protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9952
Polymers31,4661
Non-polymers5291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.901, 62.359, 107.858
Angle α, β, γ (deg.)91.781, 97.608, 111.555
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEU(chain 'A' and (resid 5 through 17 or (resid 18...AA5 - 4524 - 64
12ILEILETYRTYR(chain 'A' and (resid 5 through 17 or (resid 18...AA48 - 17667 - 195
13ALAALALYSLYS(chain 'A' and (resid 5 through 17 or (resid 18...AA179 - 259198 - 278
14OZPOZPOZPOZP(chain 'A' and (resid 5 through 17 or (resid 18...AE301
21PHEPHELEULEU(chain 'B' and (resid 5 through 46 or resid 48...BB5 - 4524 - 64
22ILEILETYRTYR(chain 'B' and (resid 5 through 46 or resid 48...BB48 - 17667 - 195
23ALAALALYSLYS(chain 'B' and (resid 5 through 46 or resid 48...BB179 - 259198 - 278
24OZPOZPOZPOZP(chain 'B' and (resid 5 through 46 or resid 48...BF301
31PHEPHELEULEU(chain 'C' and (resid 5 through 29 or (resid 30...CC5 - 4524 - 64
32ILEILETYRTYR(chain 'C' and (resid 5 through 29 or (resid 30...CC48 - 17667 - 195
33ALAALALYSLYS(chain 'C' and (resid 5 through 29 or (resid 30...CC179 - 259198 - 278
34OZPOZPOZPOZP(chain 'C' and (resid 5 through 29 or (resid 30...CG301
41PHEPHELEULEU(chain 'D' and (resid 5 through 17 or (resid 18...DD5 - 4524 - 64
42ILEILETYRTYR(chain 'D' and (resid 5 through 17 or (resid 18...DD48 - 17667 - 195
43ALAALALYSLYS(chain 'D' and (resid 5 through 17 or (resid 18...DD179 - 259198 - 278
44OZPOZPOZPOZP(chain 'D' and (resid 5 through 17 or (resid 18...DH301

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Components

#1: Protein
NNMT protein / Nicotinamide N-methyltransferase / isoform CRA_a


Mass: 31466.033 Da / Num. of mol.: 4 / Mutation: K100A, E101A, E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT, hCG_39357 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FH49, UniProt: P40261*PLUS
#2: Chemical
ChemComp-OZP / 9-(5-{[(3S)-3-amino-3-carboxypropyl][3-(3-carbamoylphenyl)propyl]amino}-5-deoxy-alpha-D-ribofuranosyl)-9H-purin-6-amine


Mass: 528.561 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H32N8O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M bicine, pH 9.0, and 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→41.47 Å / Num. obs: 48089 / % possible obs: 98.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 20.28 Å2 / CC1/2: 0.95 / Rsym value: 0.22 / Net I/σ(I): 7.64
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.8 % / Num. unique obs: 4812 / CC1/2: 0.46 / Rsym value: 0.75 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
JBluIce-EPICSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.47 Å / SU ML: 0.3182 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.8593
RfactorNum. reflection% reflection
Rfree0.2473 2007 4.17 %
Rwork0.1948 --
obs0.1969 48089 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8128 0 152 498 8778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00538488
X-RAY DIFFRACTIONf_angle_d1.044711528
X-RAY DIFFRACTIONf_chiral_restr0.06221296
X-RAY DIFFRACTIONf_plane_restr0.00781458
X-RAY DIFFRACTIONf_dihedral_angle_d11.21956002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.36281420.27773210X-RAY DIFFRACTION97.44
2.35-2.420.29231490.25243381X-RAY DIFFRACTION99.05
2.42-2.490.28111400.23463288X-RAY DIFFRACTION98.79
2.49-2.570.30581410.23073353X-RAY DIFFRACTION98.98
2.57-2.660.28951410.22483293X-RAY DIFFRACTION99.28
2.66-2.770.28861510.22513292X-RAY DIFFRACTION99.45
2.77-2.890.3051450.21773394X-RAY DIFFRACTION99.75
2.89-3.050.28321420.20863317X-RAY DIFFRACTION98.94
3.05-3.240.27361460.20773342X-RAY DIFFRACTION98.95
3.24-3.490.24481460.18723321X-RAY DIFFRACTION98.66
3.49-3.840.21181320.17142964X-RAY DIFFRACTION88.41
3.84-4.390.19551380.15423311X-RAY DIFFRACTION99.11
4.39-5.530.1691450.15273320X-RAY DIFFRACTION98.89
5.53-41.470.20471490.16593296X-RAY DIFFRACTION98.12

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